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Xu SY, Zhou L, Xu Y, Hong HY, Dai C, Wang YJ, Zheng YG. Recent advances in structure-based enzyme engineering for functional reconstruction. Biotechnol Bioeng 2023; 120:3427-3445. [PMID: 37638646 DOI: 10.1002/bit.28540] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/27/2023] [Accepted: 08/15/2023] [Indexed: 08/29/2023]
Abstract
Structural information can help engineer enzymes. Usually, specific amino acids in particular regions are targeted for functional reconstruction to enhance the catalytic performance, including activity, stereoselectivity, and thermostability. Appropriate selection of target sites is the key to structure-based design, which requires elucidation of the structure-function relationships. Here, we summarize the mutations of residues in different specific regions, including active center, access tunnels, and flexible loops, on fine-tuning the catalytic performance of enzymes, and discuss the effects of altering the local structural environment on the functions. In addition, we keep up with the recent progress of structure-based approaches for enzyme engineering, aiming to provide some guidance on how to take advantage of the structural information.
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Affiliation(s)
- Shen-Yuan Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Lei Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Ying Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Han-Yue Hong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Chen Dai
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
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Wang J, Guo X, Wan L, Liu Y, Xue H, Zhao ZK. Engineering formaldehyde dehydrogenase from Pseudomonas putida to favor nicotinamide cytosine dinucleotide. Chembiochem 2022; 23:e202100697. [PMID: 35146861 DOI: 10.1002/cbic.202100697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/09/2022] [Indexed: 11/05/2022]
Abstract
The enzyme formaldehyde dehydrogenase (FalDH) from Pseudomonas putida is of particular interest for biotechnological applications as it catalyses the oxidation of formaldehyde independent of glutathione. However, the consumption of a stoichiometric amount of nicotinamide adenine dinucleotide (NAD) can be challenging at the metabolic level as this may affect many other NAD-linked processes. A potential solution is to engineer FalDH to utilize non-natural cofactors. Here we devised FalDH variants to favor nicotinamide cytosine dinucleotide (NCD) by structure-guided modification of the binding pocket for the adenine moiety of NAD. Several mutants were obtained and the best one FalDH 9B2 had over 150-fold higher preference for NCD than NAD. Molecular docking analysis indicated that the cofactor binding pocket shrinked to better fit NCD, a smaller-sized cofactor. FalDH 9B2 together with other NCD-linked enzymes offer opportunities to assemble orthogonal pathways for biological conversion of C1 molecules.
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Affiliation(s)
- Junting Wang
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Xiaojia Guo
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Li Wan
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Yuxue Liu
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Haizhao Xue
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Zongbao Kent Zhao
- Dalian Institute of Chemical Physics, Division of Biotechnology, 457 Zhongshan Road, 116023, Dalian, CHINA
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Tan Z, Han Y, Fu Y, Zhang X, Xu M, Na Q, Zhuang W, Qu X, Ying H, Zhu C. Investigating the Structure‐Reactivity Relationships Between Nicotinamide Coenzyme Biomimetics and Pentaerythritol Tetranitrate Reductase. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Zhuotao Tan
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
| | - Yaoying Han
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
| | - Yaping Fu
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
| | - Xiaowang Zhang
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
| | - Mengjiao Xu
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
| | - Qi Na
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
| | - Wei Zhuang
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
| | - Xudong Qu
- School of Life Sciences and Biotechnology Shanghai Jiao Tong University 200240 Shanghai People's Republic of China
| | - Hanjie Ying
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
| | - Chenjie Zhu
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University 211816 Nanjing People's Republic of China
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Guo X, Wang X, Liu Y, Li Q, Wang J, Liu W, Zhao ZK. Structure-Guided Design of Formate Dehydrogenase for Regeneration of a Non-Natural Redox Cofactor. Chemistry 2020; 26:16611-16615. [PMID: 32815230 DOI: 10.1002/chem.202003102] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/12/2020] [Indexed: 12/22/2022]
Abstract
Formate dehydrogenase (FDH) has been widely used for the regeneration of the reduced nicotinamide adenine dinucleotide (NADH). To utilize nicotinamide cytosine dinucleotide (NCD) as a non-natural redox cofactor, it remains challenging as NCDH, the reduced form of NCD, has to be efficiently regenerated. Here we demonstrate successful engineering of FDH for NCDH regeneration. Guided by the structural information of FDH from Pseudomonas sp. 101 (pseFDH) and the NAD-pseFDH complex, semi-rational strategies were applied to design mutant libraries and screen for NCD-linked activity. The most active mutant reached a cofactor preference switch from NAD to NCD by 3700-fold. Homology modeling analysis showed that these mutants had reduced cofactor binding pockets and dedicated hydrophobic interactions for NCD. Efficient regeneration of NCDH was implemented by powering an NCD-dependent D-lactate dehydrogenase for stoichiometric and stereospecific reduction of pyruvate to D-lactate at the expense of formate.
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Affiliation(s)
- Xiaojia Guo
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Xueying Wang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China.,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Yuxue Liu
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Qing Li
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Junting Wang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Wujun Liu
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Zongbao K Zhao
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China.,State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China.,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
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